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Vecherskii MV, Kuznetsova TA, Khayrullin DR, Stepankov AA, Artemieva SM, Chukmasov PV, Ivanov EA, Mizin IA, Mordvintsev IN, Platonov NG, Pashali AA, Isachenko AI, Lazareva RE, Shestakova KM, Rozhnov VV. Anthropogenic Neighborhood Impact on Bacterial and Fungal Communities in Polar Bear Feces. Animals (Basel) 2023; 13:2067. [PMID: 37443865 DOI: 10.3390/ani13132067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/06/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Climate changes cause a dramatical increase in the ice-free season in the Arctic, forcing polar bears ashore, closer to human settlements associated with new and non-natural food objects. Such a diet may crucially transform the intestinal microbiome and metabolism of polar bears. The aim of this study was to characterize changes in the gut bacterial and fungal communities resulting from the transition to anthropogenic food objects by the means of 16S and ITS metabarcoding. Thus, rectal samples from 16 wild polar bears from the Kara-Barents subpopulation were studied. Human waste consuming resulted in a significant increase in the relative abundance of fermentative bacteria (Lactobacillaceae, Leuconostocaceae, and Streptococcaceae) and a decrease in proteolytic Enterobacteriaceae. However, the alpha-diversity parameters remained similar. Also, for the first time, the composition of the fungal community of the polar bear intestine was determined. Diet change is associated with the displacement of eurybiontic fungi (Thelebolus, Dipodascus, Candida (sake), and Geotrichum) by opportunistic Candida (tropicalis), Kazachstania, and Trichosporon. Feeding on human waste does not cause any signs of dysbiosis and probably leads to adaptive changes in the bacterial microbiome. However, the emergence of fungal facultative pathogens increases the risk of infections.
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Affiliation(s)
- Maksim V Vecherskii
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Tatiana A Kuznetsova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - David R Khayrullin
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Aleksandr A Stepankov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Svetlana M Artemieva
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Pavel V Chukmasov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Evgeny A Ivanov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Ivan A Mizin
- Russian Arctic National Park, Arkhangelsk 163051, Russia
| | - Ilya N Mordvintsev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikita G Platonov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | | | | | | | - Ksenia M Shestakova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
- Institute of Translational Medicine and Biotechnology, I.M. Sechenov First Moscow Medical University, Moscow 119435, Russia
| | - Viatcheslav V Rozhnov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
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Kostina NV, Chernysheva AN, Vecherskii MV, Kuznetsova TA. Microbial Nitrogen Fixation in the Intestine of Tipulidae Tipula maxima Larvae. BIOL BULL+ 2020. [DOI: 10.1134/s1062359020010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sun C, Liu H, Zhang Y, Lu C. Comparative analysis of the gut microbiota of hornbill and toucan in captivity. Microbiologyopen 2018; 8:e00786. [PMID: 30592177 PMCID: PMC6612546 DOI: 10.1002/mbo3.786] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/25/2018] [Accepted: 11/28/2018] [Indexed: 01/24/2023] Open
Abstract
Gut microbiota plays an important role in animals and are considered microbial organs. Hornbill and toucan are birds of the same ecotypes with high appreciative value. In this study, we characterized and compared the gut microbiota of toco toucan (Ramphastos toco), great hornbill (Buceros bicornis) and wreathed hornbill (Rhyticeros undulatus) using 16S rRNA high-throughput sequencing technology, and further discussed the influence of host bird genetics on its gut microbiota. We identified 10,847 operational taxonomic units (OTUs) from the hyper-variable V4-V5 region, representing 14 phyla that were dominated by the Firmicutes, Proteobacteria, Cyanobacteria, Fusobacteria, Actinobacteria, and Bacteroidetes. Alpha diversity indices showed no significant difference among the three species (p > 0.1). However, great hornbill and toco toucan shared a high number of OTUs. Principal component analysis also revealed highly similar gut microbiotas between the two distant species. Therefore, environmental factors might dominate over host genetics in shaping the gut microbiotas of hornbill and toucan. Our study would contribute in elucidating adaptation of the hornbill and toucan to environmental change.
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Affiliation(s)
- Cheng‐He Sun
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Hong‐Yi Liu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Yong Zhang
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Chang‐Hu Lu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
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García-Amado MA, Shin H, Sanz V, Lentino M, Martínez LM, Contreras M, Michelangeli F, Domínguez-Bello MG. Comparison of gizzard and intestinal microbiota of wild neotropical birds. PLoS One 2018; 13:e0194857. [PMID: 29579092 PMCID: PMC5868825 DOI: 10.1371/journal.pone.0194857] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 03/12/2018] [Indexed: 01/12/2023] Open
Abstract
Gut bacterial communities have been shown to be influenced by diet, host phylogeny and anatomy, but most of these studies have been done in captive animals. Here we compare the bacterial communities in the digestive tract of wild birds. We characterized the gizzard and intestinal microbiota among 8 wild Neotropical bird species, granivorous or frugivorous species of the orders Columbiformes and Passeriformes. We sequenced the V4 region of the 16S rRNA gene in 94 collected samples from 32 wild birds from 5 localities, and compared bacterial communities by foraging guild, organ, locality and bird taxonomy. 16S rRNA gene-based sequencing data were examined using QIIME with linear discriminant analysis effect size (LEfSe) and metabolic pathways were predicted using PICRUSt algorism. We identified 8 bacterial phyla, dominated by Firmicutes, Actinobacteria and Proteobacteria. Beta diversity analyses indicated significant separation of gut communities by bird orders (Columbiformes vs. Passerifomes) and between bird species (p<0.01). In lower intestine, PICRUSt shows a predominance of carbohydrate metabolism in granivorous birds and xenobiotics biodegradation pathways in frugivorous birds. Gizzard microbiota was significantly richer in granivorous, in relation to frugivorous birds (Chao 1; non-parametric t-test, p<0.05), suggesting a microbial gizzard function, beyond grinding food. The results suggest that the most important factor separating the bacterial community structure was bird taxonomy, followed by foraging guild. However, variation between localities is also likely to be important, but this could not been assessed with our study design.
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MESH Headings
- Algorithms
- Animals
- Animals, Wild/microbiology
- Bacteria/genetics
- Bacteria/isolation & purification
- Biodiversity
- Columbiformes/microbiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- Discriminant Analysis
- Gastrointestinal Microbiome
- Gizzard, Avian/microbiology
- Gizzard, Avian/pathology
- Intestines/microbiology
- Passeriformes/microbiology
- Principal Component Analysis
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
- Stomach Diseases/microbiology
- Stomach Diseases/pathology
- Stomach Diseases/veterinary
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Affiliation(s)
- M. Alexandra García-Amado
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto de Investigaciones Científicas (IVIC), Caracas, Venezuela
- * E-mail: (MGDB); (MAGA)
| | - Hakdong Shin
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
| | - Virginia Sanz
- Laboratorio de Biología de Organismos, Centro de Ecología, Instituto de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Miguel Lentino
- Colección Ornitológica Phelps, Apartado, Caracas, Venezuela
| | | | - Monica Contreras
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Fabian Michelangeli
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto de Investigaciones Científicas (IVIC), Caracas, Venezuela
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Nitrogenase diversity and activity in the gastrointestinal tract of the wood-eating catfish Panaque nigrolineatus. ISME JOURNAL 2015; 9:2712-24. [PMID: 25909976 PMCID: PMC4817639 DOI: 10.1038/ismej.2015.65] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/23/2015] [Accepted: 03/27/2015] [Indexed: 11/23/2022]
Abstract
The Amazonian catfish, Panaque nigrolineatus, consume large amounts of wood in their diets. The nitrogen-fixing community within the gastrointestinal (GI) tract of these catfish was found to include nifH phylotypes that are closely related to Clostridium sp., Alpha and Gammaproteobacteria, and sequences associated with GI tracts of lower termites. Fish fed a diet of sterilized palm wood were found to contain nifH messenger RNA within their GI tracts, displaying high sequence similarity to the nitrogen-fixing Bradyrhizobium group. Nitrogenase activity, measured by acetylene reduction assays, could be detected in freshly dissected GI tract material and also from anaerobic enrichment cultures propagated in nitrogen-free enrichment media; nifH sequences retrieved from these cultures were dominated by Klebsiella- and Clostridium-like sequences. Microscopic examination using catalyzed reporter deposition-enhanced immunofluorescence revealed high densities of nitrogenase-containing cells colonizing the woody digesta within the GI tract, as well as cells residing within the intestinal mucous layer. Our findings suggest that the P. nigrolineatus GI tract provides a suitable environment for nitrogen fixation that may facilitate production of reduced nitrogen by the resident microbial population under nitrogen limiting conditions. Whether this community is providing reduced nitrogen to the host in an active or passive manner and whether it is present in a permanent or transient relationship remains to be determined. The intake of a cellulose rich diet and the presence of a suitable environment for nitrogen fixation suggest that the GI tract microbial community may allow a unique trophic niche for P. nigrolineatus among fish.
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